On January 18, 2007 former National soccer team's coach Hugo Sánchez gave Magallón his first call up to the Mexican National Team, and he played his first game with the Mexican National Team on February 28, 2007. He was the player with the most Minutes at the 2007 CONCACAF Gold Cup and 2007 Copa America. On February 7, he was the protagonist of the Friendly match against the USA in the 2-2 Mexico USA match in a sold out stadium in Houston, scoring both of his side's goals. He has scored three international goals, two against USA, in a game he brought Mexico to a 2-2 draw, and a goal against Jamaica. Magallón was called up to the 2010 FIFA World Cup but he did not play in the tournament. Jonny Magallon was called up by new Mexican coach Jose Manuel de la Torre in a friendly match against Serbia on November 11, 2011.